Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

Bing Ge, Dmitry K. Pokholok, Tony Kwan, Elin Grundberg, Lisanne Morcos, Dominique J. Verlaan, Jennie Le, Vonda Koka, Kevin C.L. Lam, Vincent Gagné, Joana Dias, Rose Hoberman, Alexandre Montpetit, Marie Michele Joly, Edward J. Harvey, Daniel Sinnett, Patrick Beaulieu, Robert Hamon, Alexandru Graziani, Ken DewarEef Harmsen, Jacek Majewski, Harald H.H. Göring, Anna K. Naumova, Mathieu Blanchette, Kevin L. Gunderson, Tomi Pastinen

Research output: Contribution to journalArticlepeer-review

175 Scopus citations


Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.

Original languageEnglish (US)
Pages (from-to)1216-1222
Number of pages7
JournalNature Genetics
Issue number11
StatePublished - Nov 2009
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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